# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 14:20:19 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-amino-6-[(1S,2R)-1,2-dihydroxypropyl]pteridin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](O)c1cnc2N=C(N)NC(=O)c2n1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 BIO  BIO  2-amino-6-[(1S,2R)-1,2-dihydroxypropyl]pteridin-4(3H)-one  ligand  28  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BIO
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 BIO  N1    N  N     0  -0.505   1.2093   0.2975  -2.6753
 BIO  N2    N  NH2   0  -0.822   0.4043   0.4440  -4.8098
 BIO  C2    C  CR6   0   0.700   0.2131   0.2074  -3.5143
 BIO  N3    N  NR16  0  -0.715  -1.0594  -0.1225  -3.1337
 BIO  C4    C  CR6   0   0.538  -1.4403  -0.3940  -1.8374
 BIO  O4    O  OC    0  -0.437  -2.5842  -0.6807  -1.5549
 BIO  C4A   C  CR66  0  -0.038  -0.3288  -0.2922  -0.8937
 BIO  C8A   C  CR66  0   0.390   0.9455   0.0499  -1.3744
 BIO  N8    N  N     0  -0.388   1.9728   0.1344  -0.5111
 BIO  C7    C  CR16  0  -0.088   1.7232  -0.1014   0.7534
 BIO  C6    C  CR6   0   0.170   0.4432  -0.4357   1.2295
 BIO  N5    N  N     0  -0.392  -0.5628  -0.5273   0.3928
 BIO  C9    C  CH1   0  -0.038   0.1378  -0.6614   2.6888
 BIO  O9    O  OH1   0  -0.662  -0.8866  -1.6053   2.8461
 BIO  C10   C  CH1   0   0.011  -0.2216   0.6833   3.3554
 BIO  O10   O  OH1   0  -0.660   0.8029   1.6275   3.1256
 BIO  C11   C  CH3   0  -0.695  -0.5250   0.5197   4.8344
 BIO  HN21  H  HNH2  0   0.420   1.3279   0.6740  -5.1334
 BIO  HN22  H  HNH2  0   0.423  -0.3281   0.3594  -5.4930
 BIO  H3    H  HNR6  0   0.432  -1.7851  -0.1755  -3.8377
 BIO  H7    H  HCR6  0   0.276   2.5610  -0.0446   1.4400
 BIO  H9    H  HCH1  0   0.248   1.0294  -1.0625   3.1862
 BIO  HO9   H  HOH1  0   0.448  -1.5485  -1.4311   2.1638
 BIO  H10   H  HCH1  0   0.234  -1.1078   1.0783   2.8458
 BIO  HO1   H  HOH1  0   0.446   1.5565   1.4039   3.6831
 BIO  H111  H  HCH3  0   0.242  -0.7972   1.4783   5.2771
 BIO  H112  H  HCH3  0   0.238  -1.3513  -0.1701   4.9967
 BIO  H113  H  HCH3  0   0.224   0.3444   0.1324   5.3730

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 BIO  N1   C2    aromatic  1.306  0.020  1.306
 BIO  N1   C8A   aromatic  1.350  0.020  1.350
 BIO  N2   C2    single    1.331  0.020  1.331
 BIO  N2   HN21  single    0.860  0.020  1.020
 BIO  N2   HN22  single    0.860  0.020  1.020
 BIO  C2   N3    aromatic  1.369  0.020  1.369
 BIO  N3   C4    aromatic  1.378  0.020  1.378
 BIO  N3   H3    single    0.860  0.020  1.020
 BIO  C4   O4    double    1.213  0.020  1.213
 BIO  C4   C4A   aromatic  1.462  0.020  1.462
 BIO  C4A  C8A   aromatic  1.404  0.020  1.404
 BIO  C4A  N5    aromatic  1.329  0.020  1.329
 BIO  C8A  N8    aromatic  1.345  0.020  1.345
 BIO  N8   C7    aromatic  1.310  0.020  1.310
 BIO  C7   C6    aromatic  1.406  0.020  1.406
 BIO  C7   H7    single    0.930  0.020  1.080
 BIO  C6   N5    aromatic  1.312  0.020  1.312
 BIO  C6   C9    single    1.508  0.020  1.508
 BIO  C9   O9    single    1.402  0.020  1.402
 BIO  C9   C10   single    1.543  0.020  1.543
 BIO  C9   H9    single    0.970  0.020  1.090
 BIO  O9   HO9   single    0.850  0.020  0.980
 BIO  C10  O10   single    1.412  0.020  1.412
 BIO  C10  C11   single    1.519  0.020  1.519
 BIO  C10  H10   single    0.970  0.020  1.090
 BIO  O10  HO1   single    0.850  0.020  0.980
 BIO  C11  H111  single    0.970  0.020  1.090
 BIO  C11  H112  single    0.970  0.020  1.090
 BIO  C11  H113  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 BIO  C8A   N1   C2    117.22  3.000
 BIO  HN22  N2   HN21  118.02  3.000
 BIO  HN22  N2   C2    122.82  3.000
 BIO  HN21  N2   C2    119.09  3.000
 BIO  N3    C2   N2    116.57  3.000
 BIO  N3    C2   N1    123.19  3.000
 BIO  N2    C2   N1    120.24  3.000
 BIO  H3    N3   C4    116.47  3.000
 BIO  H3    N3   C2    119.06  3.000
 BIO  C4    N3   C2    124.48  3.000
 BIO  C4A   C4   O4    125.69  3.000
 BIO  C4A   C4   N3    112.55  3.000
 BIO  O4    C4   N3    121.76  3.000
 BIO  N5    C4A  C8A   122.30  3.000
 BIO  N5    C4A  C4    118.61  3.000
 BIO  C8A   C4A  C4    119.08  3.000
 BIO  N8    C8A  C4A   119.27  3.000
 BIO  N8    C8A  N1    117.24  3.000
 BIO  C4A   C8A  N1    123.49  3.000
 BIO  C7    N8   C8A   117.57  3.000
 BIO  H7    C7   C6    120.08  3.000
 BIO  H7    C7   N8    117.03  3.000
 BIO  C6    C7   N8    122.89  3.000
 BIO  C9    C6   N5    116.84  3.000
 BIO  C9    C6   C7    123.21  3.000
 BIO  N5    C6   C7    119.92  3.000
 BIO  C6    N5   C4A   118.05  3.000
 BIO  H9    C9   C10   108.18  3.000
 BIO  H9    C9   O9    107.27  3.000
 BIO  C10   C9   O9    111.59  3.000
 BIO  H9    C9   C6    109.21  3.000
 BIO  C10   C9   C6    109.56  3.000
 BIO  O9    C9   C6    110.94  3.000
 BIO  HO9   O9   C9    107.46  3.000
 BIO  H10   C10  C11   109.28  3.000
 BIO  H10   C10  O10   105.67  3.000
 BIO  C11   C10  O10   112.06  3.000
 BIO  H10   C10  C9    107.55  3.000
 BIO  C11   C10  C9    111.92  3.000
 BIO  O10   C10  C9    110.08  3.000
 BIO  HO1   O10  C10   108.55  3.000
 BIO  H113  C11  H112  107.80  3.000
 BIO  H113  C11  H111  108.06  3.000
 BIO  H112  C11  H111  107.88  3.000
 BIO  H113  C11  C10   111.04  3.000
 BIO  H112  C11  C10   111.41  3.000
 BIO  H111  C11  C10   110.52  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 BIO  CONST_01  C4    N3   C2   N1     0.00  0.0  0
 BIO  CONST_02  C4    C4A  C8A  N1     0.00  0.0  0
 BIO  CONST_03  N5    C4A  C8A  N1   180.00  0.0  0
 BIO  CONST_04  C7    N8   C8A  N1   180.00  0.0  0
 BIO  CONST_05  C4A   C8A  N1   C2     0.00  0.0  0
 BIO  CONST_06  N8    C8A  N1   C2   180.00  0.0  0
 BIO  CONST_07  C4A   C4   N3   C2     0.00  0.0  0
 BIO  CONST_08  C8A   N1   C2   N3     0.00  0.0  0
 BIO  CONST_09  C8A   C4A  C4   N3     0.00  0.0  0
 BIO  CONST_10  N5    C4A  C4   N3   180.00  0.0  0
 BIO  CONST_11  N8    C8A  C4A  C4   180.00  0.0  0
 BIO  CONST_12  C6    N5   C4A  C4   180.00  0.0  0
 BIO  CONST_13  C7    N8   C8A  C4A    0.00  0.0  0
 BIO  CONST_14  C7    C6   N5   C4A    0.00  0.0  0
 BIO  CONST_15  C6    N5   C4A  C8A    0.00  0.0  0
 BIO  CONST_16  C6    C7   N8   C8A    0.00  0.0  0
 BIO  CONST_17  N5    C4A  C8A  N8     0.00  0.0  0
 BIO  CONST_18  N5    C6   C7   N8     0.00  0.0  0
 BIO  CONST_19  C8A   N1   C2   N2   180.00  0.0  0
 BIO  CONST_20  C4    N3   C2   N2   180.00  0.0  0
 BIO  CONST_21  O4    C4   N3   C2   180.00  0.0  0
 BIO  CONST_22  C8A   C4A  C4   O4   180.00  0.0  0
 BIO  CONST_23  N5    C4A  C4   O4     0.00  0.0  0
 BIO  CONST_24  C9    C6   N5   C4A  180.00  0.0  0
 BIO  CONST_25  C9    C6   C7   N8   180.00  0.0  0
 BIO  CONST_26  H3    N3   C2   N1   180.00  0.0  0
 BIO  CONST_27  H7    C7   N8   C8A  180.00  0.0  0
 BIO  CONST_28  HN21  N2   C2   N1     0.00  0.0  0
 BIO  CONST_29  HN22  N2   C2   N1   180.00  0.0  0

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 BIO  chir_01  C9   C6   O9  C10  positiv
 BIO  chir_02  C10  O10  C9  C11  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 BIO  plan-1  N1    0.020
 BIO  plan-1  N2    0.020
 BIO  plan-1  C2    0.020
 BIO  plan-1  N3    0.020
 BIO  plan-1  C4    0.020
 BIO  plan-1  O4    0.020
 BIO  plan-1  C4A   0.020
 BIO  plan-1  C8A   0.020
 BIO  plan-1  N8    0.020
 BIO  plan-1  C7    0.020
 BIO  plan-1  C6    0.020
 BIO  plan-1  N5    0.020
 BIO  plan-1  C9    0.020
 BIO  plan-1  H3    0.020
 BIO  plan-1  H7    0.020
 BIO  plan-2  N2    0.020
 BIO  plan-2  C2    0.020
 BIO  plan-2  HN21  0.020
 BIO  plan-2  HN22  0.020

